Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB19151 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR614426_1.fastq.gz | Fastqsanger.gz | |||
| DRR614426_2.fastq.gz | Fastqsanger.gz | |||
| DRR614427_1.fastq.gz | Fastqsanger.gz | |||
| DRR614427_2.fastq.gz | Fastqsanger.gz | |||
| DRR614428_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:We have identified RDO5 as a phosphatase that promotes seed dormancy, most likely independent from ABA and DOG1. To obtain an indication about the genetic and molecular pathways by which RDO5 functions, we performed a transcriptomic comparison between rdo5-1 and its wild-type NIL-DOG1 at different seed stages, using the Arabidopsis Affymetrix AGRONOMICS1 tiling microarrays
2014-11-01 | GSE62578 | GEO
Project description:Abscisic acid (ABA) regulates abiotic stress and developmental responses including regulation of seed dormancy to prevent seeds from germinating under unfavorable environmental conditions. ABA HYPERSENSITIVE GERMINATION1 (AHG1) encoding a type 2C protein phosphatase (PP2C) is a central negative regulator of the ABA response in germination; however, the molecular function and regulation of AHG1 remain elusive. Here we report that AHG1 interacts with DELAY OF GERMINATION1 (DOG1), which is a pivotal positive regulator in seed dormancy. DOG1 acts upstream of AHG1 and impairs the PP2C activity of AHG1 in vitro. Furthermore, DOG1 has the ability to bind heme. Binding of DOG1 to AHG1 and heme are independent processes but both are essential for DOG1 function in vivo. Our study demonstrates that AHG1 and DOG1 constitute an important regulatory system for seed dormancy and germination by integrating multiple environmental signals, in parallel with the PYL/RCAR ABA receptor-mediated regulatory system.
2018-06-10 | PXD009392 | Pride
Project description:Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops yield visually homogenous seeds. Using automated phenotype analysis, we observed that in Arabidopsis small seeds tend to have higher primary and secondary dormancy levels when compared to large ones. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds had higher expression of translation-related genes implicated in germination competence. In contrast, small seeds showed elevated expression of many positive regulators of dormancy, including a key regulator of this process – the DOG1 gene. Differences in DOG1 expression were associated with differential production of its alternative cleavage and polyadenylation isoforms where in small seeds proximal poly(A) site is selected resulting in a short mRNA isoform. Furthermore, single-seed RNA-seq analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single seed level, the expression of genes affected by seed size was correlated with the expression of genes positioning seeds on the path towards germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species producing highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.
2023-10-16 | GSE203310 | GEO
Project description:Functional characterization of Arabidopsis WRKY15 overexpressor plants
| PRJNA125191 | ENA
Project description:Functional characterization of Taf4b in Arabidopsis thaliana
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Project description:Unveiling the signal transduction of phytohormone abscisic acid (ABA) will be greatly helpful to improve plant responses to stressful environment. ABA signaling is perceived and mediated by multi-member receptor PYR/PYLs, while whose post-translational modification, especially phosphorylation, is largely unknown. Here we demonstrated that Arabidopsis EL1-like (AEL), a casein kinase that regulates various physiological processes, phosphorylates PYR/PYLs and stimulates whose ubiquitination and degradation, leading to the suppressed ABA responses. Arabidopsis ael triple mutants display hypersensitive responses to ABA treatment, which is consistent with the suppressed degradation of PYR/PYL proteins. PYR/PYLs are phosphorylated in vivo and mutation of the conserved AEL-phosphorylation sites results in the reduced phosphorylation, ubiquitination, and degradation of PYR/PYLs, and hence the enhanced ABA responses. Our studies demonstrate the crucial roles of AEL-mediated phosphorylation in regulating the stability and function of PYR/PYLs and provide informative clues for elucidating the functional mechanism of ABA through regulating PYR/PYL receptors.
2022-02-23 | PXD008565 | Pride
Project description:This model is from the article:
A thermodynamic switch modulates abscisic acid receptor sensitivity.
Dupeux F, Santiago J, Betz K, Twycross J, Park SY, Rodriguez L, Gonzalez-Guzman M, Jensen MR, Krasnogor N, Blackledge M, Holdsworth M, Cutler SR, Rodriguez PL, Márquez JA EMBO J.
[2011 Oct; Volume: 30 (Issue: 20 )] Page info: 4171-84 21847091
,
Abstract:
Abscisic acid (ABA) is a key hormone regulating plant growth, development and the response to biotic and abiotic stress. ABA binding to pyrabactin resistance (PYR)/PYR1-like (PYL)/Regulatory Component of Abscisic acid Receptor (RCAR) intracellular receptors promotes the formation of stable complexes with certain protein phosphatases type 2C (PP2Cs), leading to the activation of ABA signalling. The PYR/PYL/RCAR family contains 14 genes in Arabidopsis and is currently the largest plant hormone receptor family known; however, it is unclear what functional differentiation exists among receptors. Here, we identify two distinct classes of receptors, dimeric and monomeric, with different intrinsic affinities for ABA and whose differential properties are determined by the oligomeric state of their apo forms. Moreover, we find a residue in PYR1, H60, that is variable between family members and plays a key role in determining oligomeric state. In silico modelling of the ABA activation pathway reveals that monomeric receptors have a competitive advantage for binding to ABA and PP2Cs. This work illustrates how receptor oligomerization can modulate hormonal responses and more generally, the sensitivity of a ligand-dependent signalling system.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1202030000 | BioModels
Project description:The SWI/SNF chromatin remodeling complex is involved in various aspects of plant development and stress responses. In this study, we investigated the role of BRM, a core subunit of the SWI/SNF complex, in seed physiological quality in Arabidopsis thaliana. We found that brm-3 seeds exhibited enlarged size, reduced yield, increased longevity, and enhanced secondary dormancy, but no change in primary dormancy or salt tolerance. We also showed that some of these phenotypes were dependent on DOG1, a key regulator of seed dormancy, as they were reversed in the brm-3xdog1-4 double mutant. Transcriptomic and metabolomic analyses revealed that BRM and DOG1 synergisticly modulate the expression of majority genes and metabolites. In contrast some of the transcriptomic and metabolomic changes including glutathione were depended on DOG1. Moreover, we demonstrated that BRM controls secondary dormancy directly through DOG1 by binding to and remodeling its 3’ region, where an antisense promoter of DOG1 is located. Our results suggest that BRM and DOG1 cooperate to control seed physiological quality by fine-tuning the chromatin state and metabolic status of seeds. This study provides new insights into the molecular mechanisms of seed dormancy and longevity, and the interplay between chromatin remodelling at DOG1 locus.
2025-01-02 | GSE251921 | GEO
Project description:Functionally complemented dog1-1 mutant with a YFP-DOG1 fusion protein under the control of its native promoter were used as starting material for in vivo pull-down of YFP: DOG1 and its interacting proteins from seed tissues in native conditions. DOG1 interacting proteins were identified by mass spectrometry. Pull-downs were performed in biological triplicates using dry or 24 h water imbibed seeds, directly after harvest (dormant condition) and after 7 months of dry storage (non-dormant condition).
2017-07-07 | PXD006347 | Pride
Project description:This model is from the article:
A thermodynamic switch modulates abscisic acid receptor sensitivit
y.
Dupeux F, Santiago J, Betz K, Twycross J, Park SY, Rodriguez L, Gonzalez-
Guzman M, Jensen MR, Krasnogor N, Blackledge M, Holdsworth M, Cutler SR, Rodrigue
z PL, Márquez JA EMBO J.
[2011 Oct; Volume: 30 (Issue: 20 )] Page info: 4171-84 21847091
,
Abstract:
Abscisic acid (ABA) is a key hormone regulating plant growth, development and the
response to biotic and abiotic stress. ABA binding to pyrabactin resistance (PYR
)/PYR1-like (PYL)/Regulatory Component of Abscisic acid Receptor (RCAR) intracell
ular receptors promotes the formation of stable complexes with certain protein ph
osphatases type 2C (PP2Cs), leading to the activation of ABA signalling. The PYR/
PYL/RCAR family contains 14 genes in Arabidopsis and is currently the largest pla
nt hormone receptor family known; however, it is unclear what functional differen
tiation exists among receptors. Here, we identify two distinct classes of recepto
rs, dimeric and monomeric, with different intrinsic affinities for ABA and whose
differential properties are determined by the oligomeric state of their apo forms
. Moreover, we find a residue in PYR1, H60, that is variable between family membe
rs and plays a key role in determining oligomeric state. In silico modelling of t
he ABA activation pathway reveals that monomeric receptors have a competitive adv
antage for binding to ABA and PP2Cs. This work illustrates how receptor oligomeri
zation can modulate hormonal responses and more generally, the sensitivity of a l
igand-dependent signalling system.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1202030001 | BioModels